The new childcare policy is due to come into force in 2015. Photograph: Alamy

More than half of working families on the lowest incomes will not qualify for the new, more generous financial support for childcare announced by the chancellor in his budget on Wednesday.

In one of the first examples of a key budget measure unravelling, the Resolution Foundation thinktank has calculated that nearly 1 million families at the bottom of the income scale will not be able to claim the extra help under the measure because one or both parents earn too little to pay income tax.

Although these households will still claim financial support at a lower level, the decision means they are not eligible for extra help of up to £26 a week for one child and £45 a week for two children that will be available to people on higher incomes. The scheme for lower earners on universal credit is separate from one aimed at people earning between £20,000 and £150,000 that provides up to £1,200 of support for childcare per child.

"The government should be applauded for attempting to help families struggling with the costs of childcare, but the truth is that those who are struggling the most are missing out," said Vidhya Alakeson, Resolution Foundation's deputy chief executive.

The two childcare schemes, briefed to newspapers before the budget, are part of the government's drive to focus on what they call "aspiration" – part of a looming election battleground with Labour over which party would do more to help "hardworking families". Both improved childcare schemes are due to come into force in autumn 2015.

The scheme for families on universal credit, being introduced this year to bring together key benefits and tax credits under a single payment, will extend the refund of childcare costs available to households from 70% currently to 85% for families in which both adults pay income tax, up to a maximum of £300 a week of childcare bills for two children.

However Resolution Foundation calculates that 900,000 families with children under 12 will not qualify for the higher rebate because one or both parents earn too little to pay income tax – ironically a tally that will increase next year when the government raises the income tax threshold to £10,000. Of these, 164,000 households have children under five.

Although the 900,000 families can still claim the 70% refund, it was still "completely wrong" that most needy families could not claim the higher rate, said Alakeson.

A Treasury source said: "The government has already taken to steps to help those working part time by removing the minimum hours rule in universal credit. We've also increased the free entitlement to 15 hours for all three- and four-year-olds and by 2014-15 [and] 260,000 two-year-olds – the most disadvantaged – will also receive 15 hours free childcare, which could be worth around £2,900 for some families."